Human Immunodeficiency Virus (HIV) is a genetically diverse virus due to frequent mutation in its genetic material. Two major genotypes exist and are designated 1 and 2. HIV type 1 (HIV-1) is most prevalent worldwide and is divided into groups and subtypes of which group M, subtype B is the most common. In the United States, other common subtypes of HIV-1 group M are: A, C, D, F, and G. In addition, genomic recombinations of these subtypes occur naturally creating circulating recombinant forms of the virus (HIV CRFs). The two most common CRFs are CRF01 (AE) and CRF02 (AG). It is believed that HIV-1 group O is less common than group M and HIV-2 is rare.
One commonly practiced approach to achieving detection of multiple genetic variants is to design probes from genomic regions which are conserved or, if that's not possible, to design multiple probes each with a different specificity. The latter approach however may lower assay sensitivity.
The ability of a biological test to detect a wide range of pathogen's genetic variants is defined as specificity. Tests with high specificity can detect large number of genetic variants in one test run and are, therefore, desirable as they offer a high level of pathogen safety and cost savings. Test sensitivity is defined as the lowest concentration of a pathogen that can be detected per unit of specimen and is often expressed numerically as LOD (limit of detection). The lower the LOD the can be difficult to develop a biological test that is both highly sensitive and specific. There is still a need, therefore, for compositions and methods for detecting HIV.